CaMELS: In silico prediction of calmodulin binding proteins and their binding sites

Due to Ca²⁺‐dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet‐lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet‐lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large‐margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM‐binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome‐wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif‐based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub‐sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels .     

Palaeoenvironmental analysis of scleractinian reef corals from the Oligo–Miocene Qom Formation in the Vartun section (northeastern Esfahan,central Iran)

This paper presents a review of palaeoenvironmental reconstructions of scleractinian corals from the Oligo–Miocene Qom Formation in northeastern Esfahan, central Iran. A total of nine genera and four species of colonial corals are identified, including Platycoenia iranica, Goniopora sp., Porites sp., Tarbellastraea reussiana, Solenastrea sp., Favites neglecta, Leptoria sp., Hydnophora cf. pulchra, Hydnophora sp., and Madracis (?) sp. These corals, all parts of massive colonies, are indicative of a reefal environment, with the main constituents, including Leptoria and Hydnophora, possessing massive meandroid, massive hydnophoroid and massive mushroom- to dome-shaped hydnophoroid colonies. The corals identified here are generally indicative of the upper photic zone and shallow water depths of less than 20 m. In the reefal environment, these corals built a wave-resistant and rigid carbonate framework in the form of a reef-front zone encapsulated by environmental conditions including low sedimentation rates and high wave energy. The occurrence of Goniopora and Porites with distinct calicles reflects clearer waters in the external part of the reefal environment.     

Classification and sensitivity analysis of the transmission dynamic of hepatitis B

Background

Hepatitis B infection caused by the hepatitis B virus is one of the most serious viral infections and a global health problem. In the transmission of hepatitis B infection, three different phases, i.e. acute infected, chronically infected, and carrier individuals, play important roles. Carrier individuals are especially significant, because they do not exhibit any symptoms and are able to transmit the infection. Here we assessed the transmissibility associated with different infection stages of hepatitis B and generated an epidemic model.

Methods

To demonstrate the transmission dynamic of hepatitis B, we investigate an epidemic model by dividing the infectious class into three subclasses, namely acute infected, chronically infected, and carrier individuals with both horizontal and vertical transmission.

Results

Numerical results and sensitivity analysis of some important parameters are presented to show that the proportion of births without successful vaccination, perinatally infected individuals, and direct contact rate are highest risk factors for the spread of hepatitis B in the community.

Conclusion

Our work provides a coherent platform for studying the full dynamics of hepatitis B and an effective direction for theoretical work.

     

Comparative Assessment on the Expression Level of Recombinant Human Follicle-Stimulating Hormone (FSH) in Serum-Containing Versus Protein-Free Culture Media

Production of recombinant pharmaceutical proteins has made a great contribution to modern biotechnology. At present, quick advances in protein expression lead to the enhancement of product quantity and quality as well as reduction in timescale processing. In the current study, we assessed the expression level of recombinant human follicle-stimulating hormone (rhFSH) in adherent and suspension Chinese hamster ovary (CHO) cell lines by cultivation in serum-containing and chemically defined, protein-free media. The expression cassette entailing FSH subunits was transfected to CHO/dhfr- and CHO DG44 cell lines, and gene amplification was achieved using dihydrofolate reductase (DHFR)/methotrexate (MTX) system. Afterward, the expression level of rhFSH was studied using real-time PCR, Western blotting and ELISA. Our achievements revealed that stepwise increase in MTX [up to 2000 nano-molar (nM)] leads to boost the expression level of rhFSH mRNA in both cell lines, although DG44 have better results, as mRNA expression level reached 124.8- and 168.3-fold in alpha and beta subunits, respectively. DG44 cells have also the best protein production in 2000 nM MTX, which reached 1.7-fold in comparison with that of the mock group. According to the above results and many advantages of protein-free media, DG44 is preferable cell line for future steps.     

A medium invasiveness multi-level patient’s specific template for pedicle screw placement in the scoliosis surgery

Background

Several methods including free-hand technique, fluoroscopic guidance, image-guided navigation, computer-assisted surgery system, robotic platform and patient’s specific templates are being used for pedicle screw placement. These methods have screw misplacements and are not always easy to be applied. Furthermore, it is necessary to expose completely a large portions of the spine in order to access fit entirely around the vertebrae.

Methods

In this study, a multi-level patient’s specific template with medium invasiveness was proposed for pedicle screw placement in the scoliosis surgery. It helps to solve the problems related to the soft tissues removal. After a computer tomography (CT) scan of the spine, the templates were designed based on surgical considerations. Each template was manufactured using three-dimensional printing technology under a semi-flexible post processing. The templates were placed on vertebras at four points—at the base of the superior-inferior articular processes on both left–right sides. This helps to obtain less invasive and more accurate procedure as well as true-stable and easy placement in a unique position. The accuracy of screw positions was confirmed by CT scan after screw placement.

Results

The result showed the correct alignment in pedicle screw placement. In addition, the template has been initially tested on a metal wire series Moulage (height 70 cm and material is PVC). The results demonstrated that it could be possible to implement it on a real patient.

Conclusions

The proposed template significantly reduced screw misplacements, increased stability, and decreased the sliding & the intervention invasiveness.

     

Thermodynamic analysis of the binding of glutathione to glutathione S-transferase over a range of temperatures.

The binding properties of a glutathione S-transferase (EC 2.5.1.18) from Schistosoma japonicum to substrate glutathione (GSH) has been investigated by intrinsic fluorescence and isothermal titration calorimetry (ITC) at pH 6.5 over a temperature range of 15-30 degrees C. Calorimetric measurements in various buffer systems with different ionization heats suggest that protons are released during the binding of GSH at pH 6.5. We have also studied the effect of pH on the thermodynamics of GSH-GST interaction. The behaviour shown at different pHs indicates that at least three groups must participate in the exchange of protons. Fluorimetric and calorimetric measurements indicate that GSH binds to two sites in the dimer of 26-kDa glutathione S-transferase from Schistosoma japonicum (SjGST). On the other hand, noncooperativity for substrate binding to SjGST was detected over a temperature range of 15-30 degrees C. Among thermodynamic parameters, whereas DeltaG degrees remains practically invariant as a function of temperature, DeltaH and DeltaS degrees both decrease with an increase in temperature. While the binding is enthalpically favorable at all temperatures studied, at temperatures below 25 degrees C, DeltaG degrees is also favoured by entropic contributions. As the temperature increases, the entropic contributions progressively decrease, attaining a value of zero at 24.3 degrees C, and then becoming unfavorable. During this transition, the enthalpic contributions become progressively favorable, resulting in an enthalpy-entropy compensation. The temperature dependence of the enthalpy change yields the heat capacity change (DeltaCp degrees ) of -0.238 +/- 0.04 kcal per K per mol of GSH bound.     

Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi

Vesicle formation at endomembranes requires the selective concentration of cargo by coat proteins. Conserved adapter protein complexes at the Golgi (AP-3), the endosome (AP-1), or the plasma membrane (AP-2) with their conserved core domain and flexible ear domains mediate this function. These complexes also rely on the small GTPase Arf1 and/or specific phosphoinositides for membrane binding. The structural details that influence these processes, however, are still poorly understood. Here we present cryo-EM structures of the full-length stable 300 kDa yeast AP-3 complex. The structures reveal that AP-3 adopts an open conformation in solution, comparable to the membrane-bound conformations of AP-1 or AP-2. This open conformation appears to be far more flexible than AP-1 or AP-2, resulting in compact, intermediate, and stretched subconformations. Mass spectrometrical analysis of the cross-linked AP-3 complex further indicates that the ear domains are flexibly attached to the surface of the complex. Using biochemical reconstitution assays, we also show that efficient AP-3 recruitment to the membrane depends primarily on cargo binding. Once bound to cargo, AP-3 clustered and immobilized cargo molecules, as revealed by single-molecule imaging on polymer-supported membranes. We conclude that its flexible open state may enable AP-3 to bind and collect cargo at the Golgi and could thus allow coordinated vesicle formation at the trans-Golgi upon Arf1 activation.

Eukaryotic cells have membrane-enclosed organelles, which carry out specialized functions, including compartmentalized biochemical reactions, metabolic channeling, and regulated signaling, inside a single cell. The transport of proteins, lipids, and other molecules between these organelles is mediated largely by small vesicular carriers that bud off at a donor compartment and fuse with the target membrane to deliver their cargo. The generation of these vesicles has been subject to extensive studies and has led to the identification of numerous coat proteins that are required for their formation at different sites (1, 2). Coat proteins can be monomers, but in most cases, they consist of several proteins, which form a heteromeric complex.Heterotetrameric adapter protein (AP) complexes are required at several endomembranes for cargo binding. Five well-conserved AP-complexes with differing functions have been identified in mammalian cells, named AP-1–AP-5, of which three (AP-1–AP-3) are conserved from yeast to human (3, 4). The three conserved adapter complexes function at different membranes along the endomembrane system. AP-1 is required for cargo transport between the Golgi and the endosome, AP-2 is required for cargo recognition and transport between the plasma membrane and the early endosome. Finally, AP-3 functions between the trans Golgi and the vacuole in yeast, whereas mammalian AP-3 localizes to a tubular endosomal compartment, in addition to or instead of the TGN (2, 5, 6).Each of the complexes consists of four different subunits: two large adaptins (named α−ζ and β1-5 respectively), a medium-sized subunit (μ1-5), and a small subunit (σ1-5). While μ- and σ-subunits together with the N-termini of the large adaptins build the membrane-binding core of the complex, the C-termini of both adaptins contain the ear domains, which are connected via flexible linkers (2). The recruitment of these complexes to membranes is not entirely conserved. They all require cargo binding, yet AP-1 binds Arf1-GTP with the γ and β1 subunit and phosphatidylinositol-4-phosphate (PI4P) via a proposed conserved site on its γ-subunit (7, 8). AP-2, on the other hand, interacts with PI(4,5)P₂ at the plasma membrane via its α, β2, and μ2 subunits (9, 10, 11).Several studies have uncovered how AP-3 functions in cargo sorting in yeast. AP-3 recognizes cargo at the Golgi via two sorting motifs in the cytosolic segments of membrane proteins: a Yxxφ sorting motif, as found in yeast in the SNARE Nyv1 or the Yck3 casein kinase, which binds to a site in μ3, as shown for mammalian AP-3, which is similar to μ2 in AP-2 (12, 13, 14), and dileucine motifs as found in the yeast SNARE Vam3 or the alkaline phosphatase Pho8, potentially also at a site comparable to AP-1 and AP-2 (15, 16). Unlike AP-1 and AP-2-coated vesicles, which depend on clathrin for their formation (2, 17), AP-3 vesicle formation in yeast does not require clathrin or the HOPS subunit Vps41 (18), yet Vps41 is required at the vacuole to bind AP-3 vesicles prior to fusion (19, 20, 21, 22). Studies in metazoan cells revealed that Vps41 and AP-3 function in regulated secretion (23, 24, 25), and AP-3 is required for biogenesis of lysosome-related organelles (26). This suggests that the AP-3 complex has features that are quite different from AP-1 and AP-2 complexes, which cooperate with clathrin in vesicle formation (2).Among the three conserved AP complexes, the function of the AP-3 complex is the least understood. Arf1 is necessary for efficient AP-3 vesicle generation in mammalian cells and shows a direct interaction with the β3 and δ subunits of AP-3 (27, 28). In addition, in vitro experiments on mammalian AP-3 using liposomes or enriched Golgi membranes suggest Arf1 as an important factor in AP-3 recruitment, whereas acidic lipids do not have a major effect, in contrast to what was found for AP-1 and AP-2 (7, 11, 29, 30). Another study showed that membrane recruitment of AP-3 depends on the recognition of sorting signals in cargo tails and PI3P (31), similar to AP-1 recruitment via cargo tails, Arf1 and PI4P (32).However, since AP-1 and AP-3 are both recruited to the trans-Golgi network (TGN) in yeast (33), the mechanism of their recruitment likely differs. Even though Arf1 is required, yeast AP-3 seems to be present at the TGN before the arrival of the Arf1 guanine nucleotide exchange factor (GEF) Sec7 (33). This implies the necessity for additional factors at the TGN and a distinct mechanism to allow for spatial and temporal separation of AP-1 and AP-3 recruitment to membranes. Structural data on mammalian AP-1 and AP-2 “core” complexes without the hinge and ear domains of their large subunits revealed that both exist in at least two very defined conformational states: a “closed” cytosolic state, where the cargo-binding sites are buried within the complex, and an “open” state, where the same sites are available to bind cargo (7, 8, 10, 34, 35). Binding of Arf1 to AP-1 or PI(4,5)P₂ in case of AP-2 induces a conformational change in the complexes that enables them to bind cargo molecules carrying a conserved acidic di-Leucine or a Tyrosine-based motif, as for all three AP complexes in yeast (8, 34). Additional conformational states and intermediates have been reported for both, mammalian AP-1 and AP-2 complex. AP-1, for example, can be hijacked by the human immunodeficiency virus-1 (HIV-1) proteins viral protein u (Vpu) and negative factor (Nef), resulting in a hyper-open conformation of AP-1 (36, 37).An emerging model over the past years has suggested that APs have several binding sites that allow for the stabilization of membrane binding and the open conformation of the complexes, but there are initial interactions required that dictate their recruitment to the target membrane. Although these interaction sites for mammalian AP-1 and AP-2 have been identified in great detail based on interaction analyses and structural studies (8, 10, 11, 35, 36, 38, 39), structural data for AP-3 is largely missing. The C-terminal part of the μ-subunit of mammalian AP-3 has been crystallized together with a Yxxφ motif-containing a cargo peptide, which revealed a similar fold and cargo-binding site as shown for AP-1 and AP-2 (14). However, positively charged binding surfaces required for PIP-interaction were not well conserved. Although the “trunk” segment of AP-1 and AP-2 is known quite well by now, information on hinge and ear domains in context of these complexes is largely missing. Crystal structures of the isolated ear domains of α-, γ- and β2-adaptin have been published (40, 41, 42), and a study on mammalian AP-3 suggested a direct interaction between δ-ear and δ3 that interfered with Arf1-binding (43). Furthermore, during tethering of AP-3 vesicles with the yeast vacuole, the δ−subunit Apl5 of the yeast AP-3 complex binds to the Vps41 subunit of the HOPS complex as a prerequisite of fusion (18, 19, 21, 22).In this study, we applied single particle electron cryo-microscopy (cryo-EM) to analyze the purified full-length AP-3 complex from yeast and unraveled the factors required for AP-3 recruitment to membranes by biochemical reconstitution. Our data reveal that a surprisingly flexible AP-3 complex requires a combination of cargo, PI4P, and Arf1 for membrane binding, which explains its function in selective cargo sorting at the Golgi.